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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccactatttgttttttgtactaagaaccaaaaaaaagggttttcggacgccttacattcagaggttaactagcagctctaaatttacttcgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTCTAGAACATCCAAGATCAAAGGAGCTGACAGAAGCACCAATCTCATGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g46750.4
intron # 15
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18387976|gb|BM421174.1|BM421174
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCANAATGAGCTCGCCATGCCGT
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCA-AATGAGCTCGCCATGCCGT
EST: gi|88376684|gb|CI537988.1|CI537988
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACNACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88473320|gb|CI410591.1|CI410591
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|87031853|gb|CI272554.1|CI272554
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATAGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|86851760|gb|CI316329.1|CI316329
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|38481557|gb|CF965646.1|CF965646
EST:     TTAGTCGAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88297470|gb|CI547948.1|CI547948
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|87020943|gb|CI269660.1|CI269660
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACCACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88383770|gb|CI545921.1|CI545921
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88477920|gb|CI415191.1|CI415191
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTAGTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|86862327|gb|CI330209.1|CI330209
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGGTGCCAAATGAGCTCGCCATGCCTT
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAG-TGCCAAATGAGCTCGCCATGCCGT
EST: gi|86425938|gb|CI071035.1|CI071035
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88447311|gb|CI533952.1|CI533952
EST:     TTACTCCAACATATAAAAANAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTG
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88838591|gb|CI375139.1|CI375139
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAA-TGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88489629|gb|CI426901.1|CI426901
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|29618099|gb|CB623111.1|CB623111
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|88515706|gb|CI443360.1|CI443360
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
EST: gi|27548326|gb|CA766515.2|CA766515
EST:     TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAG                         GGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC
genomic: TTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 71 (downstream exon)
Score: 39

AAAGGCTGTACATCTTGAACCAGTGCCATTTGACATGGACCGTGATTTGATTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctca ... cgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTCTAGAACATCCAAGATCAAAGGAGCTGACAGAAGCACCAATCTCATGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacgccttacattcagaggttaactagcagctctaaatttacttcgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTCTAGAACATCCAAGATCAAAGGAGCTGACAGAAGCACCAATCTCATGCTG
                               ctctaaa  putative branch site (score: 39)
                                      tttacttc  CT-rich tract
                                  taaatttactt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccactatttgttttttgtactaagaaccaaaaaaaagggttttcggacgccttacattcagaggttaactagcagctctaaatttacttcgatttgcagGGAACAATTGACAACATGTACAGAAGTGCCAAATGAGCTCGCCATGCCGTCTAGAACATCCAAGATCAAAGGAGCTGACAGAAGCACCAATCTCATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG